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Conserved domains on  [gi|85675194|dbj|BAA15849|]
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antitoxin of the YoeB-YefM toxin-antitoxin system [Escherichia coli str. K-12 substr. W3110]

Protein Classification

type II toxin-antitoxin system Phd/YefM family antitoxin( domain architecture ID 10013794)

type II toxin-antitoxin (TA) system Phd/YefM family antitoxin similar to Escherichia coli YefM, the antitoxin component of the YoeB-YefM TA module that counteracts the effect of the YoeB toxin; YefM binds to the promoter region of the yefM-yeoB operon to repress transcription

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11409 PRK11409
YoeB-YefM toxin-antitoxin system antitoxin YefM;
1-83 5.16e-46

YoeB-YefM toxin-antitoxin system antitoxin YefM;


:

Pssm-ID: 171099  Cd Length: 83  Bit Score: 141.60  E-value: 5.16e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85675194   1 MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKD 80
Cdd:PRK11409  1 MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKD 80


                ...
gi 85675194  81 IIE 83
Cdd:PRK11409 81 IIE 83
 
Name Accession Description Interval E-value
PRK11409 PRK11409
YoeB-YefM toxin-antitoxin system antitoxin YefM;
1-83 5.16e-46

YoeB-YefM toxin-antitoxin system antitoxin YefM;


Pssm-ID: 171099  Cd Length: 83  Bit Score: 141.60  E-value: 5.16e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85675194   1 MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKD 80
Cdd:PRK11409  1 MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKD 80


                ...
gi 85675194  81 IIE 83
Cdd:PRK11409 81 IIE 83
StbD COG2161
Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense ...
 1-83 2.62e-35

Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense mechanisms];


Pssm-ID: 441764  Cd Length: 83  Bit Score: 114.50  E-value: 2.62e-35
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85675194  1 MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKD 80
Cdd:COG2161  1 MTTISYSEARKNLASLLDQVVEDHEPVIITRRNGPAAVLISAEDYESLQETLYLLSSPANAERLLESLAELEAGEVSLDE 80


               ...
gi 85675194 81 IIE 83
Cdd:COG2161 81 LIE 83
PhdYeFM_antitox pfam02604
Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins ...
 1-66 1.67e-20

Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins in type II toxin-antitoxin systems. When bound to their toxin partners, they can bind DNA via the N-terminus and repress the expression of operons containing genes encoding the toxin and the antitoxin. This domain complexes with Txe toxins containing pfam06769, Fic/DOC toxins containing pfam02661 and YafO toxins containing pfam13957.


Pssm-ID: 460615  Cd Length: 67  Bit Score: 76.91  E-value: 1.67e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 85675194    1 MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEE-TAYLLRSPANARRLMD 66
Cdd:pfam02604  1 MKIVSISEARNNLSELLDEVEDGGEPVIITRRGKPVAVLLSLEDYERLQElTLYLLSLPANAERLAE 67
phd_fam TIGR01552
prevent-host-death family protein; This model recognizes a region of about 55 amino acids ...
 3-55 3.40e-09

prevent-host-death family protein; This model recognizes a region of about 55 amino acids toward the N-terminal end of bacterial proteins of about 85 amino acids in length. The best-characterized member is prevent-host-death (phd) of bacteriophage P1, the antidote partner of death-on-curing (doc) (TIGR01550) in an addiction module. Addiction modules prevent plasmid curing by killing the host cell as the longer-lived killing protein persists while the gene for the shorter-lived antidote is lost. Note, however, that relatively few members of this family appear to be plasmid or phage-encoded. Also, there is little overlap, except for phage P1 itself, of species with this family and with the doc family. [Cellular processes, Toxin production and resistance, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 273688  Cd Length: 52  Bit Score: 47.66  E-value: 3.40e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 85675194    3 TISYSEARQNLSaTMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLL 55
Cdd:TIGR01552  1 SVSLSEAKNKLG-ELLKRVRDGEPVTITKRGRPVAVLVSAADYDRLQETLRLL 52
 
Name Accession Description Interval E-value
PRK11409 PRK11409
YoeB-YefM toxin-antitoxin system antitoxin YefM;
1-83 5.16e-46

YoeB-YefM toxin-antitoxin system antitoxin YefM;


Pssm-ID: 171099  Cd Length: 83  Bit Score: 141.60  E-value: 5.16e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85675194   1 MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKD 80
Cdd:PRK11409  1 MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKD 80


                ...
gi 85675194  81 IIE 83
Cdd:PRK11409 81 IIE 83
StbD COG2161
Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense ...
 1-83 2.62e-35

Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense mechanisms];


Pssm-ID: 441764  Cd Length: 83  Bit Score: 114.50  E-value: 2.62e-35
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85675194  1 MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTEKD 80
Cdd:COG2161  1 MTTISYSEARKNLASLLDQVVEDHEPVIITRRNGPAAVLISAEDYESLQETLYLLSSPANAERLLESLAELEAGEVSLDE 80


               ...
gi 85675194 81 IIE 83
Cdd:COG2161 81 LIE 83
PhdYeFM_antitox pfam02604
Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins ...
 1-66 1.67e-20

Antitoxin Phd_YefM, type II toxin-antitoxin system; Members of this family act as antitoxins in type II toxin-antitoxin systems. When bound to their toxin partners, they can bind DNA via the N-terminus and repress the expression of operons containing genes encoding the toxin and the antitoxin. This domain complexes with Txe toxins containing pfam06769, Fic/DOC toxins containing pfam02661 and YafO toxins containing pfam13957.


Pssm-ID: 460615  Cd Length: 67  Bit Score: 76.91  E-value: 1.67e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 85675194    1 MRTISYSEARQNLSATMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEE-TAYLLRSPANARRLMD 66
Cdd:pfam02604  1 MKIVSISEARNNLSELLDEVEDGGEPVIITRRGKPVAVLLSLEDYERLQElTLYLLSLPANAERLAE 67
phd_fam TIGR01552
prevent-host-death family protein; This model recognizes a region of about 55 amino acids ...
 3-55 3.40e-09

prevent-host-death family protein; This model recognizes a region of about 55 amino acids toward the N-terminal end of bacterial proteins of about 85 amino acids in length. The best-characterized member is prevent-host-death (phd) of bacteriophage P1, the antidote partner of death-on-curing (doc) (TIGR01550) in an addiction module. Addiction modules prevent plasmid curing by killing the host cell as the longer-lived killing protein persists while the gene for the shorter-lived antidote is lost. Note, however, that relatively few members of this family appear to be plasmid or phage-encoded. Also, there is little overlap, except for phage P1 itself, of species with this family and with the doc family. [Cellular processes, Toxin production and resistance, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 273688  Cd Length: 52  Bit Score: 47.66  E-value: 3.40e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 85675194    3 TISYSEARQNLSaTMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLL 55
Cdd:TIGR01552  1 SVSLSEAKNKLG-ELLKRVRDGEPVTITKRGRPVAVLVSAADYDRLQETLRLL 52
Phd COG4118
Antitoxin component of toxin-antitoxin stability system, DNA-binding transcriptional repressor ...
 1-71 5.40e-06

Antitoxin component of toxin-antitoxin stability system, DNA-binding transcriptional repressor [Defense mechanisms];


Pssm-ID: 443294 [Multi-domain]  Cd Length: 65  Bit Score: 39.92  E-value: 5.40e-06
                       10        20        30        40        50        60        70
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 85675194  1 MRTISYSEARQNLSAtMMKAVEDHAPILITRQNGEACVLMSLEEYNSLEETAYLlrspanARRLMDSIDSL 71
Cdd:COG4118  1 MKTVTVREAKAHLSE-LLDRVEAGEEVVITRRGKPVARLVPVEPPRRPRALGLL------KGRLSDDFDEP 64
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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